Tumor DNA
Genomic DNA samples were obtained from the tumor using the ZYMO Research Quick-DNARNA FFPE MiniPrep Kit (Cat# R1009 Lot# 207499), and following the user manual of the ZYMO Research Quick-DNARNA FFPE MiniPrep kit. RNase was used to remove RNA during DNA extraction. DNA samples were sequenced using the Novaseq S4 sequencing system (150 bp paired-end reads, over 800 million reads per sample). Reads were trimmed using the cutadapt tool, followed by alignment to the hg38 genome using the Dragen pipeline.